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    An Integrated Graph-Theoretic Approach to Understanding Solvation Using a Novel Data Mining Tool, moleculaRnetworks

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    Author
    Mooney, Barbara Logan
    Issue Date
    2012
    Keywords
    networks
    solvation
    Chemistry
    data mining
    hydrogen bond
    Advisor
    Corrales, L. René
    
    Metadata
    Show full item record
    Publisher
    The University of Arizona.
    Rights
    Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
    Embargo
    Release after 21-Aug-2013
    Abstract
    An integrated graph-theoretic and geometric approach to the analysis of aqueous solvation of atomic ions is presented. This analysis makes use of a novel data-mining tool, moleculaRnetworks, to process data from molecular dynamics simulations. The workings and structure of this tool are discussed, along with the development and testing of its PageRank algorithm-based rapid solvation polyhedra classifier. The ability to classify instantaneous solvation polyhedra enables a finely detailed understanding of shell structure-behavior relationships, as water molecules simultaneously rearrange about ions, exchange with the bulk, and rearrange their hydrogen-bond network. The application of the tool to cation systems, including lithium, sodium, potassium, magnesium, calcium, and lanthanum, yields new insight into the mechanisms of water exchange about these ions. It is shown that in order for exchange events to occur, the solvation shell must "preorganize" to admit or expel a molecule of water: this preorganization is reflected in the mechanistic preference for each ion. The application of the tool to anion systems, including fluoride, chloride, and bromide, reveals that these ions have an extended effect on the reorientation ability of water molecules beyond their first solvation shell. Finally, when both ions are present, as in the potential of mean force simulation between lanthanum and chloride, structural rearrangements can be seen as the ions break through the barrier to form the contact ion pair. Taken together, these results show the utility of the moleculaRnetworks tool in broadening our understanding of aqueous ion solvation.
    Type
    text
    Electronic Dissertation
    Degree Name
    Ph.D.
    Degree Level
    doctoral
    Degree Program
    Graduate College
    Chemistry
    Degree Grantor
    University of Arizona
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